rcorces
commented
1 year ago Hi @fe4960! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
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fe4960
Hello,
Attach your log file This step doesn't generate a log file.
Describe the bug I tried to subset a ArchR project with the code below:
proj2=subsetArchRProject( ArchRProj = proj1, cells = final_cell, outputDirectory = dir, dropCells = TRUE)
It generated the error below and didn't went through:
Copying ArchRProject to new outputDirectory : human_meta/data/proj4_clean1_final Copying Arrow Files... Error in .safelapply(seq_along(inArrows), function(x) { : Error Found Iteration 51 : [1] "Error in
[.data.frame(.h5read(inArrow, h5name), idxKeep) : \n undefined columns selected\n" <simpleError in[.data.frame(.h5read(inArrow, h5name), idxKeep): undefined columns selected> Calls: subsetArchRProject ... saveArchRProject -> .copyArrows -> unlist -> .safelapply In addition: Warning message: In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) : 1 function calls resulted in an error Execution haltedI used the latest version of ArchR v1.0.3, as v1.0.2 generated other error. I used the same code with v1.0.3 to run through other datasets and worked well. I wonder what causes the error in this dataset and if you can help fix it. Thanks a lot!
I searched the previous issues and found this error has not been solved before.
Session Info R version 4.1.0 (2021-05-18)
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 grid stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] rhdf5_2.38.1 SummarizedExperiment_1.24.0 [3] Biobase_2.54.0 RcppArmadillo_0.11.0.0.0
[5] Rcpp_1.0.9 Matrix_1.5-3
[7] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[9] IRanges_2.28.0 S4Vectors_0.32.4
[11] BiocGenerics_0.40.0 sparseMatrixStats_1.6.0
[13] MatrixGenerics_1.6.0 matrixStats_0.63.0
[15] data.table_1.14.6 stringr_1.5.0
[17] plyr_1.8.8 magrittr_2.0.3
[19] ggplot2_3.4.0 gtable_0.3.1
[21] gtools_3.9.4 gridExtra_2.3
[23] devtools_2.4.4 usethis_2.1.6
[25] ArchR_1.0.3
loaded via a namespace (and not attached): [1] pkgload_1.3.0 shiny_1.7.1 assertthat_0.2.1
[4] GenomeInfoDbData_1.2.7 remotes_2.4.2 sessioninfo_1.2.2
[7] pillar_1.7.0 lattice_0.20-45 glue_1.6.2
[10] digest_0.6.30 promises_1.2.0.1 XVector_0.34.0
[13] colorspace_2.0-3 htmltools_0.5.2 httpuv_1.6.5
[16] pkgconfig_2.0.3 zlibbioc_1.40.0 purrr_0.3.4
[19] xtable_1.8-4 scales_1.2.1 processx_3.5.3
[22] later_1.3.0 tibble_3.1.6 generics_0.1.2
[25] ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0
[28] cli_3.5.0 crayon_1.5.2 mime_0.12
[31] memoise_2.0.1 ps_1.6.0 fs_1.5.2
[34] fansi_1.0.3 pkgbuild_1.3.1 profvis_0.3.7
[37] tools_4.1.0 prettyunits_1.1.1 lifecycle_1.0.3
[40] Rhdf5lib_1.16.0 munsell_0.5.0 DelayedArray_0.20.0
[43] callr_3.7.0 compiler_4.1.0 rlang_1.0.6
[46] RCurl_1.98-1.9 rhdf5filters_1.6.0 htmlwidgets_1.5.4
[49] miniUI_0.1.1.1 bitops_1.0-7 DBI_1.1.3
[52] R6_2.5.1 dplyr_1.0.8 fastmap_1.1.0
[55] utf8_1.2.2 stringi_1.7.8 parallel_4.1.0
[58] vctrs_0.5.1 tidyselect_1.1.2 urlchecker_1.0.1